Details of assembly methods and in silico genotyping for Salmonella

  • All MLST-like typing methods in EnteroBase are derived from a genome assembly of sequenced reads. For an explanation of this method, see here
  • For a general description of the in silico typing method, see here
MLST – Classic Ribosomal MLST (Jolley, 2012) Core Genome MLST Whole Genome MLST
7 Loci 53 Loci 3,002 Loci 21,065 Loci
Conserved Housekeeping genes Ribosomal proteins Core genes Any coding sequence
Highly conserved; Low resolution Highly conserved; Medium resolution Variable; High resolution Highly variable; Extreme resolution
Different scheme for each species/genus Single scheme across tree of life Different scheme for each species/genus Different scheme for each species/genus

7 Gene MLST

Classic MLST scheme is described in Kidgell et al (2002) Infection, Genetics and Evolution. 2(1) 39-45.

Genes included in 7 gene MLST (together with the length of sequence used for MLST taken from table 1 in the above cited paper):

Gene Name/ Locus Tag Length
thrA STY0002 501
purE STY0582 399
sucA STY0779 501
hisD STY2281 501
aroC STY2616 501
hemD STY3622 432
dnaN STY3941 501

Ribosomal MLST (rMLST)